Change Graph class behavior

[peterhys]

Description

Changed the Graph class behavior in adding nodes, updated the docstrings and documentation, and add issue and pull request templates.

Type of Change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Code refactoring
• Performance improvement
• Test improvement

Changes Made

• Change .set_node_object and .set_node_object_from to .add_node_object and .add_node_objects_from in the Graph class
• Modify documentation and docstrings
• Add "CONTRIBUTE.rst" for contribution guidelines
• Add issue and pull request guideline

Testing

• All existing tests pass
• New tests added for new features/bug fixes

Documentation

• Documentation has been updated
• Code examples added/updated
• Docstrings added/updated
• No documentation changes needed

Checklist

• My code follows the project's style guidelines (PEP 8, black formatting)
• I have commented my code where necessary
• My changes generate no new warnings or errors